This repository contains the functionality to standardize the data of Boets et al. (2016) to both a Darwin Core checklist and Darwin Core occurrence dataset that can be harvested by GBIF. The repository also contains the code for a website to explore the occurrence data. It was developed for the TrIAS project.
- Checklist dataset: source data → Darwin Core mapping script → generated Darwin Core files
- Occurrence dataset: source data → Darwin Core mapping script → generated Darwin Core files
The repository structure is based on Cookiecutter Data Science and the Checklist recipe. Files and directories indicated with GENERATED should not be edited manually.
├── README.md : Description of this repository
├── LICENSE : Repository license
├── alien-macroinvertebrates.Rproj : RStudio project file
├── .gitignore : Files and directories to be ignored by git
│
├── data
│ ├── raw : Source data, input for mapping script
│ └── processed : Darwin Core output of mapping script GENERATED
│
├── docs : Repository website GENERATED
│
├── specifications : Data specifications for the Darwin Core files
│
└── src
├── dwc_checklist.Rmd : Darwin Core mapping script for checklist dataset
├── dwc_occurrence.Rmd : Darwin Core mapping script for occurrence dataset
├── _site.yml : Settings to build website in docs/
└── index.Rmd : Template for website homepage
- Clone this repository to your computer
- Open the RStudio project file
- Open the
dwc_checklist.Rmdordwc_occurrence.RmdR Markdown file in RStudio - Install any required packages
- Click
Run > Run Allto generate the processed data - Alternatively, click
Build > Build websiteto generate the processed data and build the website indocs/